MATLAB

MATLAB is a technical computing environment for high-performance numeric computation and visualization. MATLAB integrates numerical analysis, matrix computation, signal processing, and graphics in an easy-to-use environment where problems and solutions are expressed just as they are written mathematically--without traditional programming.

Availability and Restrictions

Versions

MATLAB is available on Oakley, Ruby, and Owens Clusters. The versions currently available at OSC are:

Version

Ruby

Owens

pitzer

notes

2014a

X

Default version on Ruby prior to 09/15/2015

2014b

X

2015a

X

2015b

X

X

2016b

X

X

2017a

X

X

2018a

X*

X*

X*

2018b

X

X

X

* Current default version

You can use module spider matlab to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access: Academic Users Only (non-commercial, non-government)

Any academic users at OSC can use Matlab. All users must be added to the license server before using MATLAB. Please contact OSC Help to be granted access.

Publisher/Vendor/Repository and License Type

MathWorks, Commercial (University site license)

Usage

Usage on Ruby

Set-up

To load the default version of MATLAB module, use module load matlab . For a list of all available MATLAB versions and the format expected, type: module spider matlab . To select a particular software version, use module load matlab/version . For example, use module load matlab/r2014b to load MATLAB version 2014b.

Running MATLAB

The following command will start an interactive, command line version of MATLAB:

matlab -nodisplay

If you are able to use X-11 forwarding and have enabled it in your SSH client software preferences, you can run MATLAB using the GUI by typing the command matlab . For more information about the matlab command usage, type matlab –h for a complete list of command line options.

The commands listed above will run MATLAB on the login node you are connected to. As the login node is a shared resource, running scripts that require significant computational resources will impact the usability of the cluster for others. As such, you should not use interactive MATLAB sessions on the login node for any significant computation. If your MATLAB script requires significant time, CPU power, or memory, you should run your code via the batch system.

Batch Usage

When you log into ruby.osc.edu you are actually logged into a Linux box referred to as the login node. To gain access to the multiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request multiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info.

Interactive Batch Session

For an interactive batch session using the command line version of MATLAB, one can run the following command:

qsub -I -X -l nodes=1:ppn=20 -l walltime=00:20:00

which requests one whole node with 20 cores ( -l nodes=1:ppn=20 ), for a walltime of 20 minutes ( -l walltime=00:20:00 ). Here you can run MATLAB interactively by loading the MATLAB module and running MATLAB with the options of your choice as described above. The –X flag enables X11 forwarding on the compute node, so you can use the MATLAB GUI if you choose.You may adjust the numbers per your need.

Parallel Processing in MATLAB

MATLAB supports implicit multithreading on a single node.

Multithreading

Multithreading allows some functions in MATLAB to distribute the work load between cores of the node that your job is running on. By default, all of the current versions of MATLAB available on the OSC clusters have multithreading enabled.

Multithreading increases the speed of some linear algebra routines, but if you would like to disable multithreading you may include the option " -singleCompThread " when running MATLAB. An example is given below:

Usage on Owens

Set-up

To load the default version of MATLAB module, use module load matlab . For a list of all available MATLAB versions and the format expected, type: module spider matlab . To select a particular software version, use module load matlab/version . For example, use module load matlab/r2015b to load MATLAB version r2015b.

Running MATLAB

The following command will start an interactive, command line version of MATLAB:

matlab -nodisplay

If you are able to use X-11 forwarding and have enabled it in your SSH client software preferences, you can run MATLAB using the GUI by typing the command matlab . For more information about the matlab command usage, type matlab –h for a complete list of command line options.

The commands listed above will run MATLAB on the login node you are connected to. As the login node is a shared resource, running scripts that require significant computational resources will impact the usability of the cluster for others. As such, you should not use interactive MATLAB sessions on the login node for any significant computation. If your MATLAB script requires significant time, CPU power, or memory, you should run your code via the batch system.

Batch Usage

When you log into owens.osc.edu you are actually logged into a Linux box referred to as the login node. To gain access to the multiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request multiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info.

Interactive Batch Session

For an interactive batch session using the command line version of MATLAB, one can run the following command:

qsub -I -X -l nodes=1:ppn=28 -l walltime=00:20:00

which requests one whole node with 28 cores ( -l nodes=1:ppn=28 ), for a walltime of 20 minutes ( -l walltime=00:20:00 ). Here you can run MATLAB interactively by loading the MATLAB module and running MATLAB with the options of your choice as described above. The –X flag enables X11 forwarding on the compute node, so you can use the MATLAB GUI if you choose.You may adjust the numbers per your need.

Parallel Processing in MATLAB

MATLAB supports implicit multithreading on a single node.

Multithreading

Multithreading allows some functions in MATLAB to distribute the work load between cores of the node that your job is running on. By default, all of the current versions of MATLAB available on the OSC clusters have multithreading enabled.

Multithreading increases the speed of some linear algebra routines, but if you would like to disable multithreading you may include the option " -singleCompThread " when running MATLAB. An example is given below:

Usage on Pitzer

Set-up

To load the default version of MATLAB module, use module load matlab.

Running MATLAB

The following command will start an interactive, command line version of MATLAB:

matlab -nodisplay

If you are able to use X-11 forwarding and have enabled it in your SSH client software preferences, you can run MATLAB using the GUI by typing the command matlab. For more information about the matlab command usage, type matlab –h for a complete list of command line options.

The commands listed above will run MATLAB on the login node you are connected to. As the login node is a shared resource, running scripts that require significant computational resources will impact the usability of the cluster for others. As such, you should not use interactive MATLAB sessions on the login node for any significant computation. If your MATLAB script requires significant time, CPU power, or memory, you should run your code via the batch system.

Batch Usage

When you log into pitzer.osc.edu you are actually logged into a Linux box referred to as the login node. To gain access to the multiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request multiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info.

Interactive Batch Session

For an interactive batch session using the command line version of MATLAB, one can run the following command:

qsub -I -X -l nodes=1:ppn=28 -l walltime=00:20:00

which requests one whole node with 28 cores ( -l nodes=1:ppn=28 ), for a walltime of 20 minutes ( -l walltime=00:20:00 ). Here you can run MATLAB interactively by loading the MATLAB module and running MATLAB with the options of your choice as described above. The –X flag enables X11 forwarding on the compute node, so you can use the MATLAB GUI if you choose.You may adjust the numbers per your need.

Parallel Processing in MATLAB

MATLAB supports implicit multithreading on a single node.

Multithreading

Multithreading allows some functions in MATLAB to distribute the work load between cores of the node that your job is running on. By default, all of the current versions of MATLAB available on the OSC clusters have multithreading enabled.

The system will run as many threads as there are cores on the nodes requested. For the normal nodes, this mean matlab will start 28 threads to run on the 28 cores of the node.

Multithreading increases the speed of some linear algebra routines, but if you would like to disable multithreading you may include the option " -singleCompThread" when running MATLAB. An example is given below:

MATLAB with a GPU

A GPU can be utilized for MATLAB. You can acquire a GPU by nodes=1:ppn=20;gpus=1 for Ruby or Owens (ppn=28 for Owens). For more detail, please read here.

You can check the GPU assigned to you using:

gpuDeviceCount # show how many GPUs you have
gpuDevice # show the details of the GPU

You can replace an array to gpuArray, for example:

A = gpuArray(A)

where A is a regular MATLAB array. This transfers the array data to the GPU memory. Then, you can use the gpuArray variable in GPU supported built-in functions. You can find the full list of GPU supported built-in functions from here. For more information about GPU programming for MATLAB, please read "GPU Computing" from Mathworks.

Toolboxes and Features

OSC's current licenses support the following MATLAB toolboxes and features (please contact OSC Help for license-specific questions):